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J Proteome Res. 2016 Aug 5;15(8):2812-25. doi: 10.1021/acs.jproteome.6b00378. Epub 2016 Jul 25.

Comprehensive Proteomic Analysis of Nitrogen-Starved Mycobacterium smegmatis Δpup Reveals the Impact of Pupylation on Nitrogen Stress Response.

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Institute of Medical Microbiology, University of Zurich , Zurich, Switzerland.
Institute of Molecular Medicine and Cell Research, University of Freiburg , Freiburg, Germany.
Functional Genomic Center, University of Zurich/ETH , Zurich, Switzerland.
BIOSS Centre for Biological Signaling Studies, University of Freiburg , Freiburg, Germany.
Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg , Freiburg, Germany.
Faculty of Biology, University of Freiburg , Freiburg, Germany.
German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) , Heidelberg, Germany.


Pupylation is a bacterial ubiquitin-like protein modification pathway, which results in the attachment of the small protein Pup to specific lysine residues of cellular targets. Pup was shown to serve as a degradation signal, directing proteins toward the bacterial proteasome for turnover. Recently, it was hypothesized that pupylation and proteasomal protein degradation support the survival of Mycobacterium smegmatis (Msm) during nitrogen starvation by supplying recycled amino acids. In the present study we generated a Pup deletion strain to investigate the influence of pupylation on Msm proteome in the absence of nitrogen sources. Quantitative proteomic analyses revealed a relatively low impact of Pup on MsmΔpup proteome immediately after exposure to growth medium lacking nitrogen. Less than 5.4% of the proteins displayed altered cellular levels when compared to Msm wild type. In contrast, post 24 h of nitrogen starvation 501 proteins (41% of the total quantified proteome) of Msm pup deletion strain showed significant changes in abundance. Noteworthy, important players involved in nitrogen assimilation were significantly affected in MsmΔpup. Furthermore, we quantified pupylated proteins of nitrogen-starved Msm to gain more detailed insights in the role of pupylation in surviving and overcoming the lack of nitrogen.


Mycobacterium smegmatis; nitrogen starvation; pupylation; quantitative proteomics

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